Multiple sequence alignment - TraesCS2D01G518200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G518200 chr2D 100.000 3533 0 0 1 3533 608560378 608556846 0.000000e+00 6525
1 TraesCS2D01G518200 chr2D 87.922 2310 170 47 551 2836 608578806 608576582 0.000000e+00 2619
2 TraesCS2D01G518200 chr2A 91.068 2407 174 20 641 3030 740079359 740076977 0.000000e+00 3216
3 TraesCS2D01G518200 chr2A 90.182 2037 171 17 641 2659 740143391 740141366 0.000000e+00 2627
4 TraesCS2D01G518200 chr2A 90.034 2037 174 17 641 2659 740119203 740117178 0.000000e+00 2610
5 TraesCS2D01G518200 chr2A 92.857 336 6 4 3058 3378 740076981 740076649 4.130000e-129 472
6 TraesCS2D01G518200 chr2B 92.190 2087 113 22 638 2707 742110636 742108583 0.000000e+00 2905
7 TraesCS2D01G518200 chr2B 91.376 1890 139 7 658 2545 742173066 742171199 0.000000e+00 2566
8 TraesCS2D01G518200 chr2B 91.197 852 50 9 2701 3533 742105120 742104275 0.000000e+00 1134
9 TraesCS2D01G518200 chr7B 84.169 2653 308 62 565 3172 525598890 525596305 0.000000e+00 2470
10 TraesCS2D01G518200 chr7B 81.275 251 33 10 2676 2918 525941700 525941456 1.290000e-44 191
11 TraesCS2D01G518200 chr7A 86.646 2209 237 31 1000 3172 563246816 563244630 0.000000e+00 2392
12 TraesCS2D01G518200 chr7A 87.680 1940 203 25 1000 2918 563293364 563291440 0.000000e+00 2226
13 TraesCS2D01G518200 chr7D 88.758 1779 170 13 1000 2765 497320719 497318958 0.000000e+00 2150
14 TraesCS2D01G518200 chr7D 79.252 294 37 16 2480 2757 497345979 497345694 2.170000e-42 183


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G518200 chr2D 608556846 608560378 3532 True 6525.0 6525 100.0000 1 3533 1 chr2D.!!$R1 3532
1 TraesCS2D01G518200 chr2D 608576582 608578806 2224 True 2619.0 2619 87.9220 551 2836 1 chr2D.!!$R2 2285
2 TraesCS2D01G518200 chr2A 740141366 740143391 2025 True 2627.0 2627 90.1820 641 2659 1 chr2A.!!$R2 2018
3 TraesCS2D01G518200 chr2A 740117178 740119203 2025 True 2610.0 2610 90.0340 641 2659 1 chr2A.!!$R1 2018
4 TraesCS2D01G518200 chr2A 740076649 740079359 2710 True 1844.0 3216 91.9625 641 3378 2 chr2A.!!$R3 2737
5 TraesCS2D01G518200 chr2B 742171199 742173066 1867 True 2566.0 2566 91.3760 658 2545 1 chr2B.!!$R1 1887
6 TraesCS2D01G518200 chr2B 742104275 742110636 6361 True 2019.5 2905 91.6935 638 3533 2 chr2B.!!$R2 2895
7 TraesCS2D01G518200 chr7B 525596305 525598890 2585 True 2470.0 2470 84.1690 565 3172 1 chr7B.!!$R1 2607
8 TraesCS2D01G518200 chr7A 563244630 563246816 2186 True 2392.0 2392 86.6460 1000 3172 1 chr7A.!!$R1 2172
9 TraesCS2D01G518200 chr7A 563291440 563293364 1924 True 2226.0 2226 87.6800 1000 2918 1 chr7A.!!$R2 1918
10 TraesCS2D01G518200 chr7D 497318958 497320719 1761 True 2150.0 2150 88.7580 1000 2765 1 chr7D.!!$R1 1765

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
506 507 0.177141 AAACCATCCATGCATGCAGC 59.823 50.0 26.69 0.0 45.96 5.25 F
940 959 0.179018 ACTTCGTTGAGCCAAGCCTT 60.179 50.0 0.00 0.0 0.00 4.35 F
941 960 0.519077 CTTCGTTGAGCCAAGCCTTC 59.481 55.0 0.00 0.0 0.00 3.46 F
942 961 0.889186 TTCGTTGAGCCAAGCCTTCC 60.889 55.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1469 0.472925 TGGGTAGGTGCAGGAGTTGA 60.473 55.000 0.00 0.00 0.0 3.18 R
2251 2283 1.048601 AACCTATCATCGGCGTGGAT 58.951 50.000 17.11 17.11 0.0 3.41 R
2256 2288 1.202533 ACCTCAAACCTATCATCGGCG 60.203 52.381 0.00 0.00 0.0 6.46 R
2819 6365 1.257415 CTTCTTGATCGAGATGCGTGC 59.743 52.381 13.61 0.00 41.8 5.34 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.987046 GCTATGCGCAAATACAGGTTC 58.013 47.619 17.11 0.00 38.92 3.62
42 43 2.354510 GCTATGCGCAAATACAGGTTCA 59.645 45.455 17.11 0.00 38.92 3.18
43 44 3.546815 GCTATGCGCAAATACAGGTTCAG 60.547 47.826 17.11 0.00 38.92 3.02
44 45 1.890876 TGCGCAAATACAGGTTCAGT 58.109 45.000 8.16 0.00 0.00 3.41
45 46 2.226330 TGCGCAAATACAGGTTCAGTT 58.774 42.857 8.16 0.00 0.00 3.16
46 47 2.621055 TGCGCAAATACAGGTTCAGTTT 59.379 40.909 8.16 0.00 0.00 2.66
47 48 3.234386 GCGCAAATACAGGTTCAGTTTC 58.766 45.455 0.30 0.00 0.00 2.78
48 49 3.304391 GCGCAAATACAGGTTCAGTTTCA 60.304 43.478 0.30 0.00 0.00 2.69
49 50 4.466828 CGCAAATACAGGTTCAGTTTCAG 58.533 43.478 0.00 0.00 0.00 3.02
50 51 4.229876 GCAAATACAGGTTCAGTTTCAGC 58.770 43.478 0.00 0.00 0.00 4.26
51 52 4.261572 GCAAATACAGGTTCAGTTTCAGCA 60.262 41.667 0.00 0.00 0.00 4.41
52 53 5.215160 CAAATACAGGTTCAGTTTCAGCAC 58.785 41.667 0.00 0.00 0.00 4.40
53 54 2.418368 ACAGGTTCAGTTTCAGCACA 57.582 45.000 0.00 0.00 0.00 4.57
54 55 2.017049 ACAGGTTCAGTTTCAGCACAC 58.983 47.619 0.00 0.00 0.00 3.82
55 56 2.016318 CAGGTTCAGTTTCAGCACACA 58.984 47.619 0.00 0.00 0.00 3.72
56 57 2.620115 CAGGTTCAGTTTCAGCACACAT 59.380 45.455 0.00 0.00 0.00 3.21
57 58 3.067180 CAGGTTCAGTTTCAGCACACATT 59.933 43.478 0.00 0.00 0.00 2.71
58 59 3.701040 AGGTTCAGTTTCAGCACACATTT 59.299 39.130 0.00 0.00 0.00 2.32
59 60 4.160252 AGGTTCAGTTTCAGCACACATTTT 59.840 37.500 0.00 0.00 0.00 1.82
60 61 4.869861 GGTTCAGTTTCAGCACACATTTTT 59.130 37.500 0.00 0.00 0.00 1.94
93 94 9.745018 TTTCTTCTGAAATGATAATTGTCTCCT 57.255 29.630 3.72 0.00 37.27 3.69
94 95 8.954950 TCTTCTGAAATGATAATTGTCTCCTC 57.045 34.615 3.72 0.00 0.00 3.71
95 96 8.542926 TCTTCTGAAATGATAATTGTCTCCTCA 58.457 33.333 3.72 3.00 0.00 3.86
96 97 9.339850 CTTCTGAAATGATAATTGTCTCCTCAT 57.660 33.333 3.72 0.00 0.00 2.90
97 98 9.690913 TTCTGAAATGATAATTGTCTCCTCATT 57.309 29.630 3.72 0.00 37.98 2.57
98 99 9.334947 TCTGAAATGATAATTGTCTCCTCATTC 57.665 33.333 3.72 1.18 35.96 2.67
99 100 9.339850 CTGAAATGATAATTGTCTCCTCATTCT 57.660 33.333 3.72 0.00 35.96 2.40
100 101 9.690913 TGAAATGATAATTGTCTCCTCATTCTT 57.309 29.630 3.72 0.00 35.96 2.52
104 105 9.917887 ATGATAATTGTCTCCTCATTCTTTTCT 57.082 29.630 3.72 0.00 0.00 2.52
109 110 9.972106 AATTGTCTCCTCATTCTTTTCTAAGAT 57.028 29.630 0.00 0.00 40.01 2.40
110 111 8.783833 TTGTCTCCTCATTCTTTTCTAAGATG 57.216 34.615 0.00 0.00 40.01 2.90
111 112 7.334090 TGTCTCCTCATTCTTTTCTAAGATGG 58.666 38.462 0.00 0.00 40.01 3.51
112 113 6.259829 GTCTCCTCATTCTTTTCTAAGATGGC 59.740 42.308 0.00 0.00 40.01 4.40
113 114 6.157645 TCTCCTCATTCTTTTCTAAGATGGCT 59.842 38.462 0.00 0.00 40.01 4.75
114 115 6.725364 TCCTCATTCTTTTCTAAGATGGCTT 58.275 36.000 0.00 0.00 40.01 4.35
115 116 6.825721 TCCTCATTCTTTTCTAAGATGGCTTC 59.174 38.462 0.00 0.00 40.01 3.86
116 117 6.600822 CCTCATTCTTTTCTAAGATGGCTTCA 59.399 38.462 3.03 0.00 40.01 3.02
117 118 7.121759 CCTCATTCTTTTCTAAGATGGCTTCAA 59.878 37.037 3.03 0.00 40.01 2.69
118 119 8.585471 TCATTCTTTTCTAAGATGGCTTCAAT 57.415 30.769 3.03 0.00 40.01 2.57
119 120 9.685276 TCATTCTTTTCTAAGATGGCTTCAATA 57.315 29.630 3.03 0.00 40.01 1.90
122 123 9.466497 TTCTTTTCTAAGATGGCTTCAATATGT 57.534 29.630 3.03 0.00 40.01 2.29
123 124 9.466497 TCTTTTCTAAGATGGCTTCAATATGTT 57.534 29.630 3.03 0.00 35.49 2.71
126 127 8.806429 TTCTAAGATGGCTTCAATATGTTTCA 57.194 30.769 3.03 0.00 35.56 2.69
127 128 8.442632 TCTAAGATGGCTTCAATATGTTTCAG 57.557 34.615 3.03 0.00 35.56 3.02
128 129 8.267183 TCTAAGATGGCTTCAATATGTTTCAGA 58.733 33.333 3.03 0.00 35.56 3.27
129 130 6.939132 AGATGGCTTCAATATGTTTCAGAG 57.061 37.500 3.03 0.00 0.00 3.35
130 131 6.421485 AGATGGCTTCAATATGTTTCAGAGT 58.579 36.000 3.03 0.00 0.00 3.24
131 132 7.568349 AGATGGCTTCAATATGTTTCAGAGTA 58.432 34.615 3.03 0.00 0.00 2.59
132 133 8.216423 AGATGGCTTCAATATGTTTCAGAGTAT 58.784 33.333 3.03 0.00 0.00 2.12
133 134 7.558161 TGGCTTCAATATGTTTCAGAGTATG 57.442 36.000 0.00 0.00 0.00 2.39
134 135 7.112122 TGGCTTCAATATGTTTCAGAGTATGT 58.888 34.615 0.00 0.00 0.00 2.29
135 136 7.280876 TGGCTTCAATATGTTTCAGAGTATGTC 59.719 37.037 0.00 0.00 0.00 3.06
136 137 7.254932 GGCTTCAATATGTTTCAGAGTATGTCC 60.255 40.741 0.00 0.00 0.00 4.02
137 138 7.280876 GCTTCAATATGTTTCAGAGTATGTCCA 59.719 37.037 0.00 0.00 0.00 4.02
138 139 9.334947 CTTCAATATGTTTCAGAGTATGTCCAT 57.665 33.333 0.00 0.00 0.00 3.41
139 140 9.685276 TTCAATATGTTTCAGAGTATGTCCATT 57.315 29.630 0.00 0.00 0.00 3.16
140 141 9.112725 TCAATATGTTTCAGAGTATGTCCATTG 57.887 33.333 0.00 0.00 0.00 2.82
141 142 8.896744 CAATATGTTTCAGAGTATGTCCATTGT 58.103 33.333 0.00 0.00 0.00 2.71
142 143 9.466497 AATATGTTTCAGAGTATGTCCATTGTT 57.534 29.630 0.00 0.00 0.00 2.83
144 145 8.862325 ATGTTTCAGAGTATGTCCATTGTTAA 57.138 30.769 0.00 0.00 0.00 2.01
145 146 8.322906 TGTTTCAGAGTATGTCCATTGTTAAG 57.677 34.615 0.00 0.00 0.00 1.85
146 147 7.936847 TGTTTCAGAGTATGTCCATTGTTAAGT 59.063 33.333 0.00 0.00 0.00 2.24
147 148 8.784043 GTTTCAGAGTATGTCCATTGTTAAGTT 58.216 33.333 0.00 0.00 0.00 2.66
148 149 8.547967 TTCAGAGTATGTCCATTGTTAAGTTC 57.452 34.615 0.00 0.00 0.00 3.01
149 150 7.676004 TCAGAGTATGTCCATTGTTAAGTTCA 58.324 34.615 0.00 0.00 0.00 3.18
150 151 7.819415 TCAGAGTATGTCCATTGTTAAGTTCAG 59.181 37.037 0.00 0.00 0.00 3.02
151 152 7.819415 CAGAGTATGTCCATTGTTAAGTTCAGA 59.181 37.037 0.00 0.00 0.00 3.27
152 153 8.543774 AGAGTATGTCCATTGTTAAGTTCAGAT 58.456 33.333 0.00 0.00 0.00 2.90
153 154 8.498054 AGTATGTCCATTGTTAAGTTCAGATG 57.502 34.615 0.00 0.00 0.00 2.90
154 155 6.764308 ATGTCCATTGTTAAGTTCAGATGG 57.236 37.500 0.00 0.00 36.29 3.51
155 156 5.630121 TGTCCATTGTTAAGTTCAGATGGT 58.370 37.500 0.00 0.00 36.35 3.55
156 157 5.473162 TGTCCATTGTTAAGTTCAGATGGTG 59.527 40.000 0.00 0.00 36.35 4.17
157 158 4.458989 TCCATTGTTAAGTTCAGATGGTGC 59.541 41.667 0.00 0.00 36.35 5.01
158 159 4.380867 CCATTGTTAAGTTCAGATGGTGCC 60.381 45.833 0.00 0.00 31.61 5.01
159 160 3.500448 TGTTAAGTTCAGATGGTGCCA 57.500 42.857 0.00 0.00 0.00 4.92
160 161 3.826524 TGTTAAGTTCAGATGGTGCCAA 58.173 40.909 0.00 0.00 0.00 4.52
161 162 3.568007 TGTTAAGTTCAGATGGTGCCAAC 59.432 43.478 0.00 0.00 0.00 3.77
171 172 3.264574 GGTGCCAACCTATGCTTGA 57.735 52.632 0.00 0.00 43.84 3.02
172 173 1.767759 GGTGCCAACCTATGCTTGAT 58.232 50.000 0.00 0.00 43.84 2.57
173 174 2.930950 GGTGCCAACCTATGCTTGATA 58.069 47.619 0.00 0.00 43.84 2.15
174 175 3.287222 GGTGCCAACCTATGCTTGATAA 58.713 45.455 0.00 0.00 43.84 1.75
175 176 3.699038 GGTGCCAACCTATGCTTGATAAA 59.301 43.478 0.00 0.00 43.84 1.40
176 177 4.159506 GGTGCCAACCTATGCTTGATAAAA 59.840 41.667 0.00 0.00 43.84 1.52
177 178 5.163416 GGTGCCAACCTATGCTTGATAAAAT 60.163 40.000 0.00 0.00 43.84 1.82
178 179 6.340522 GTGCCAACCTATGCTTGATAAAATT 58.659 36.000 0.00 0.00 0.00 1.82
179 180 6.818142 GTGCCAACCTATGCTTGATAAAATTT 59.182 34.615 0.00 0.00 0.00 1.82
180 181 7.978975 GTGCCAACCTATGCTTGATAAAATTTA 59.021 33.333 0.00 0.00 0.00 1.40
181 182 8.703743 TGCCAACCTATGCTTGATAAAATTTAT 58.296 29.630 0.00 0.00 0.00 1.40
182 183 9.546428 GCCAACCTATGCTTGATAAAATTTATT 57.454 29.630 0.00 0.00 0.00 1.40
217 218 8.794335 AGACTTTTAACTTTGTCAAAGAGAGT 57.206 30.769 28.07 20.90 41.02 3.24
218 219 9.886132 AGACTTTTAACTTTGTCAAAGAGAGTA 57.114 29.630 28.07 13.17 41.02 2.59
219 220 9.917872 GACTTTTAACTTTGTCAAAGAGAGTAC 57.082 33.333 28.07 13.85 41.02 2.73
220 221 9.444600 ACTTTTAACTTTGTCAAAGAGAGTACA 57.555 29.630 28.07 8.06 41.02 2.90
226 227 9.614792 AACTTTGTCAAAGAGAGTACATAGTTT 57.385 29.630 28.07 7.54 39.48 2.66
265 266 6.331369 TCAAGCTCTTGATTTAGTTTTGGG 57.669 37.500 8.14 0.00 43.90 4.12
266 267 5.833131 TCAAGCTCTTGATTTAGTTTTGGGT 59.167 36.000 8.14 0.00 43.90 4.51
267 268 5.712152 AGCTCTTGATTTAGTTTTGGGTG 57.288 39.130 0.00 0.00 0.00 4.61
268 269 4.524328 AGCTCTTGATTTAGTTTTGGGTGG 59.476 41.667 0.00 0.00 0.00 4.61
269 270 4.522789 GCTCTTGATTTAGTTTTGGGTGGA 59.477 41.667 0.00 0.00 0.00 4.02
270 271 5.010617 GCTCTTGATTTAGTTTTGGGTGGAA 59.989 40.000 0.00 0.00 0.00 3.53
271 272 6.462347 GCTCTTGATTTAGTTTTGGGTGGAAA 60.462 38.462 0.00 0.00 0.00 3.13
272 273 7.610580 TCTTGATTTAGTTTTGGGTGGAAAT 57.389 32.000 0.00 0.00 0.00 2.17
273 274 8.713708 TCTTGATTTAGTTTTGGGTGGAAATA 57.286 30.769 0.00 0.00 0.00 1.40
274 275 8.581578 TCTTGATTTAGTTTTGGGTGGAAATAC 58.418 33.333 0.00 0.00 0.00 1.89
275 276 7.841282 TGATTTAGTTTTGGGTGGAAATACA 57.159 32.000 0.00 0.00 0.00 2.29
276 277 8.429237 TGATTTAGTTTTGGGTGGAAATACAT 57.571 30.769 0.00 0.00 0.00 2.29
277 278 8.875168 TGATTTAGTTTTGGGTGGAAATACATT 58.125 29.630 0.00 0.00 0.00 2.71
385 386 6.932356 TTCCATTGACTAGGTAGTAGTACG 57.068 41.667 1.63 0.00 42.48 3.67
386 387 5.994250 TCCATTGACTAGGTAGTAGTACGT 58.006 41.667 7.96 7.96 42.48 3.57
387 388 6.418101 TCCATTGACTAGGTAGTAGTACGTT 58.582 40.000 8.15 0.00 42.48 3.99
388 389 6.886459 TCCATTGACTAGGTAGTAGTACGTTT 59.114 38.462 8.15 0.00 42.48 3.60
389 390 7.066284 TCCATTGACTAGGTAGTAGTACGTTTC 59.934 40.741 8.15 6.53 42.48 2.78
390 391 7.148188 CCATTGACTAGGTAGTAGTACGTTTCA 60.148 40.741 8.15 8.65 42.48 2.69
391 392 7.928307 TTGACTAGGTAGTAGTACGTTTCAT 57.072 36.000 8.15 0.00 42.48 2.57
392 393 7.312657 TGACTAGGTAGTAGTACGTTTCATG 57.687 40.000 8.15 0.00 42.48 3.07
393 394 6.881065 TGACTAGGTAGTAGTACGTTTCATGT 59.119 38.462 8.15 1.81 42.48 3.21
394 395 8.040727 TGACTAGGTAGTAGTACGTTTCATGTA 58.959 37.037 8.15 0.00 42.48 2.29
395 396 8.202745 ACTAGGTAGTAGTACGTTTCATGTAC 57.797 38.462 8.15 0.00 40.47 2.90
396 397 6.111768 AGGTAGTAGTACGTTTCATGTACG 57.888 41.667 17.32 17.32 43.48 3.67
405 406 4.770351 CGTTTCATGTACGTATGATGCA 57.230 40.909 0.00 0.00 36.97 3.96
406 407 5.328886 CGTTTCATGTACGTATGATGCAT 57.671 39.130 0.00 0.00 36.97 3.96
407 408 5.132576 CGTTTCATGTACGTATGATGCATG 58.867 41.667 2.46 13.97 36.97 4.06
408 409 5.051106 CGTTTCATGTACGTATGATGCATGA 60.051 40.000 17.22 17.22 42.54 3.07
411 412 6.470557 TCATGTACGTATGATGCATGAATG 57.529 37.500 18.28 0.00 41.68 2.67
412 413 6.222389 TCATGTACGTATGATGCATGAATGA 58.778 36.000 18.28 0.00 41.68 2.57
413 414 6.875195 TCATGTACGTATGATGCATGAATGAT 59.125 34.615 18.28 0.00 41.68 2.45
414 415 7.388500 TCATGTACGTATGATGCATGAATGATT 59.612 33.333 18.28 0.00 41.68 2.57
415 416 8.658609 CATGTACGTATGATGCATGAATGATTA 58.341 33.333 2.46 0.00 39.21 1.75
416 417 8.776376 TGTACGTATGATGCATGAATGATTAT 57.224 30.769 2.46 0.00 0.00 1.28
417 418 8.658609 TGTACGTATGATGCATGAATGATTATG 58.341 33.333 2.46 0.00 0.00 1.90
418 419 7.910441 ACGTATGATGCATGAATGATTATGA 57.090 32.000 2.46 0.00 0.00 2.15
419 420 7.745972 ACGTATGATGCATGAATGATTATGAC 58.254 34.615 2.46 0.00 0.00 3.06
420 421 7.148356 ACGTATGATGCATGAATGATTATGACC 60.148 37.037 2.46 0.00 0.00 4.02
421 422 5.970317 TGATGCATGAATGATTATGACCC 57.030 39.130 2.46 0.00 0.00 4.46
422 423 4.456566 TGATGCATGAATGATTATGACCCG 59.543 41.667 2.46 0.00 0.00 5.28
423 424 2.553602 TGCATGAATGATTATGACCCGC 59.446 45.455 0.00 0.00 0.00 6.13
424 425 2.553602 GCATGAATGATTATGACCCGCA 59.446 45.455 0.00 0.00 0.00 5.69
425 426 3.192001 GCATGAATGATTATGACCCGCAT 59.808 43.478 0.00 0.00 41.08 4.73
426 427 4.729595 CATGAATGATTATGACCCGCATG 58.270 43.478 0.00 0.00 37.87 4.06
427 428 4.084011 TGAATGATTATGACCCGCATGA 57.916 40.909 0.00 0.00 37.87 3.07
428 429 4.654915 TGAATGATTATGACCCGCATGAT 58.345 39.130 0.00 0.00 37.87 2.45
429 430 5.803552 TGAATGATTATGACCCGCATGATA 58.196 37.500 0.00 0.00 37.87 2.15
430 431 6.417258 TGAATGATTATGACCCGCATGATAT 58.583 36.000 0.00 0.00 37.87 1.63
431 432 6.885918 TGAATGATTATGACCCGCATGATATT 59.114 34.615 0.00 0.00 37.87 1.28
432 433 7.394077 TGAATGATTATGACCCGCATGATATTT 59.606 33.333 0.00 0.00 37.87 1.40
433 434 8.806429 AATGATTATGACCCGCATGATATTTA 57.194 30.769 0.00 0.00 37.87 1.40
434 435 7.609760 TGATTATGACCCGCATGATATTTAC 57.390 36.000 0.00 0.00 37.87 2.01
435 436 7.394016 TGATTATGACCCGCATGATATTTACT 58.606 34.615 0.00 0.00 37.87 2.24
436 437 8.536175 TGATTATGACCCGCATGATATTTACTA 58.464 33.333 0.00 0.00 37.87 1.82
437 438 8.718102 ATTATGACCCGCATGATATTTACTAC 57.282 34.615 0.00 0.00 37.87 2.73
438 439 5.801531 TGACCCGCATGATATTTACTACT 57.198 39.130 0.00 0.00 0.00 2.57
439 440 5.779922 TGACCCGCATGATATTTACTACTC 58.220 41.667 0.00 0.00 0.00 2.59
440 441 5.148651 ACCCGCATGATATTTACTACTCC 57.851 43.478 0.00 0.00 0.00 3.85
441 442 4.838986 ACCCGCATGATATTTACTACTCCT 59.161 41.667 0.00 0.00 0.00 3.69
442 443 6.014647 ACCCGCATGATATTTACTACTCCTA 58.985 40.000 0.00 0.00 0.00 2.94
443 444 6.668283 ACCCGCATGATATTTACTACTCCTAT 59.332 38.462 0.00 0.00 0.00 2.57
444 445 6.980978 CCCGCATGATATTTACTACTCCTATG 59.019 42.308 0.00 0.00 0.00 2.23
445 446 6.477033 CCGCATGATATTTACTACTCCTATGC 59.523 42.308 0.00 0.00 35.22 3.14
446 447 7.035612 CGCATGATATTTACTACTCCTATGCA 58.964 38.462 0.00 0.00 37.60 3.96
447 448 7.221645 CGCATGATATTTACTACTCCTATGCAG 59.778 40.741 0.00 0.00 37.60 4.41
448 449 8.037758 GCATGATATTTACTACTCCTATGCAGT 58.962 37.037 0.00 0.00 37.65 4.40
449 450 9.935241 CATGATATTTACTACTCCTATGCAGTT 57.065 33.333 0.00 0.00 0.00 3.16
450 451 9.935241 ATGATATTTACTACTCCTATGCAGTTG 57.065 33.333 0.00 0.00 0.00 3.16
451 452 9.143155 TGATATTTACTACTCCTATGCAGTTGA 57.857 33.333 0.00 0.00 0.00 3.18
459 460 9.314133 ACTACTCCTATGCAGTTGATAATATGA 57.686 33.333 0.00 0.00 0.00 2.15
462 463 9.851686 ACTCCTATGCAGTTGATAATATGAAAA 57.148 29.630 0.00 0.00 0.00 2.29
469 470 9.340695 TGCAGTTGATAATATGAAAAAGAAACG 57.659 29.630 0.00 0.00 0.00 3.60
470 471 9.554724 GCAGTTGATAATATGAAAAAGAAACGA 57.445 29.630 0.00 0.00 0.00 3.85
481 482 7.659652 TGAAAAAGAAACGAATTTTTGTGGT 57.340 28.000 0.00 0.00 38.40 4.16
482 483 8.758633 TGAAAAAGAAACGAATTTTTGTGGTA 57.241 26.923 0.00 0.00 38.40 3.25
483 484 9.204570 TGAAAAAGAAACGAATTTTTGTGGTAA 57.795 25.926 0.00 0.00 38.40 2.85
484 485 9.467990 GAAAAAGAAACGAATTTTTGTGGTAAC 57.532 29.630 0.00 0.00 38.40 2.50
485 486 6.799786 AAGAAACGAATTTTTGTGGTAACG 57.200 33.333 0.00 0.00 42.51 3.18
486 487 6.121613 AGAAACGAATTTTTGTGGTAACGA 57.878 33.333 0.00 0.00 42.51 3.85
487 488 6.553524 AGAAACGAATTTTTGTGGTAACGAA 58.446 32.000 0.00 0.00 42.51 3.85
488 489 7.028361 AGAAACGAATTTTTGTGGTAACGAAA 58.972 30.769 0.00 0.00 37.81 3.46
499 500 2.490115 TGGTAACGAAAACCATCCATGC 59.510 45.455 4.54 0.00 42.10 4.06
500 501 2.490115 GGTAACGAAAACCATCCATGCA 59.510 45.455 0.00 0.00 36.96 3.96
501 502 3.130340 GGTAACGAAAACCATCCATGCAT 59.870 43.478 0.00 0.00 36.96 3.96
502 503 2.945447 ACGAAAACCATCCATGCATG 57.055 45.000 20.19 20.19 0.00 4.06
503 504 1.135024 ACGAAAACCATCCATGCATGC 60.135 47.619 21.69 11.82 0.00 4.06
504 505 1.135053 CGAAAACCATCCATGCATGCA 60.135 47.619 25.04 25.04 0.00 3.96
505 506 2.546778 GAAAACCATCCATGCATGCAG 58.453 47.619 26.69 16.97 0.00 4.41
506 507 0.177141 AAACCATCCATGCATGCAGC 59.823 50.000 26.69 0.00 45.96 5.25
507 508 1.682451 AACCATCCATGCATGCAGCC 61.682 55.000 26.69 0.00 44.83 4.85
508 509 2.734591 CATCCATGCATGCAGCCC 59.265 61.111 26.69 0.00 44.83 5.19
509 510 2.523412 ATCCATGCATGCAGCCCC 60.523 61.111 26.69 0.00 44.83 5.80
510 511 4.845447 TCCATGCATGCAGCCCCC 62.845 66.667 26.69 0.00 44.83 5.40
589 591 1.097547 CAGCCGGATGGTGACCAATC 61.098 60.000 13.14 6.95 45.48 2.67
591 593 1.097547 GCCGGATGGTGACCAATCAG 61.098 60.000 9.06 7.71 36.95 2.90
630 632 2.360350 CGCCTGGATGGTGCTGTT 60.360 61.111 0.00 0.00 39.73 3.16
631 633 2.401766 CGCCTGGATGGTGCTGTTC 61.402 63.158 0.00 0.00 39.73 3.18
632 634 1.303561 GCCTGGATGGTGCTGTTCA 60.304 57.895 0.00 0.00 38.35 3.18
633 635 0.682209 GCCTGGATGGTGCTGTTCAT 60.682 55.000 0.00 0.00 38.35 2.57
634 636 1.386533 CCTGGATGGTGCTGTTCATC 58.613 55.000 0.00 0.00 39.08 2.92
636 638 2.397751 GGATGGTGCTGTTCATCCG 58.602 57.895 6.59 0.00 46.52 4.18
653 655 2.728817 GGCAGTATCCGGACCGAG 59.271 66.667 17.49 5.68 0.00 4.63
656 658 1.813859 CAGTATCCGGACCGAGCAA 59.186 57.895 17.49 0.00 0.00 3.91
865 874 0.892358 AGCAGCAAAGCAAGCTAGCA 60.892 50.000 18.83 0.00 41.14 3.49
883 895 2.766828 AGCAAATTACTAGCTCCTCCGT 59.233 45.455 0.00 0.00 32.05 4.69
897 912 3.162666 TCCTCCGTTTCTTCTTGCTCTA 58.837 45.455 0.00 0.00 0.00 2.43
900 915 1.390463 CCGTTTCTTCTTGCTCTACGC 59.610 52.381 0.00 0.00 39.77 4.42
904 919 0.532573 TCTTCTTGCTCTACGCCAGG 59.467 55.000 0.00 0.00 38.05 4.45
926 945 3.949031 GCTACCTAGCTCCACTTCG 57.051 57.895 0.00 0.00 45.62 3.79
929 948 2.735762 GCTACCTAGCTCCACTTCGTTG 60.736 54.545 0.00 0.00 45.62 4.10
937 956 0.884704 TCCACTTCGTTGAGCCAAGC 60.885 55.000 0.00 0.00 0.00 4.01
938 957 1.576421 CACTTCGTTGAGCCAAGCC 59.424 57.895 0.00 0.00 0.00 4.35
939 958 0.886490 CACTTCGTTGAGCCAAGCCT 60.886 55.000 0.00 0.00 0.00 4.58
940 959 0.179018 ACTTCGTTGAGCCAAGCCTT 60.179 50.000 0.00 0.00 0.00 4.35
941 960 0.519077 CTTCGTTGAGCCAAGCCTTC 59.481 55.000 0.00 0.00 0.00 3.46
942 961 0.889186 TTCGTTGAGCCAAGCCTTCC 60.889 55.000 0.00 0.00 0.00 3.46
943 962 2.335712 CGTTGAGCCAAGCCTTCCC 61.336 63.158 0.00 0.00 0.00 3.97
944 963 1.075659 GTTGAGCCAAGCCTTCCCT 59.924 57.895 0.00 0.00 0.00 4.20
945 964 0.962855 GTTGAGCCAAGCCTTCCCTC 60.963 60.000 0.00 0.00 0.00 4.30
946 965 1.136329 TTGAGCCAAGCCTTCCCTCT 61.136 55.000 3.42 0.00 0.00 3.69
947 966 1.077858 GAGCCAAGCCTTCCCTCTG 60.078 63.158 0.00 0.00 0.00 3.35
984 1016 5.249780 TGCTCCTAATCAAGGGTTAAACA 57.750 39.130 0.00 0.00 46.55 2.83
996 1028 6.999871 TCAAGGGTTAAACAACCTACCTAAAG 59.000 38.462 6.51 0.00 42.44 1.85
1065 1097 3.039588 GACAAGGCGGCGTTCGAA 61.040 61.111 9.37 0.00 42.43 3.71
1437 1469 2.264166 GCTCTCGACTGGCTTGCT 59.736 61.111 0.00 0.00 0.00 3.91
1448 1480 1.601759 GGCTTGCTCAACTCCTGCA 60.602 57.895 0.00 0.00 34.69 4.41
1689 1721 1.219664 CTTCGACCCCGCCAACATA 59.780 57.895 0.00 0.00 35.37 2.29
2130 2162 2.868583 CGATCTTAAGGACATGCAGGTG 59.131 50.000 9.62 0.00 0.00 4.00
2251 2283 4.588106 TGGCCAAGATGTTTGAAGATTTCA 59.412 37.500 0.61 0.00 38.04 2.69
2256 2288 6.810182 CCAAGATGTTTGAAGATTTCATCCAC 59.190 38.462 0.00 0.00 39.84 4.02
2338 2370 1.375908 GCAAGTGGAGCCATGACGA 60.376 57.895 0.00 0.00 0.00 4.20
2819 6365 1.012998 CGAGTGACGAATGCATGCG 60.013 57.895 25.67 25.67 45.77 4.73
2839 6389 1.257415 GCACGCATCTCGATCAAGAAG 59.743 52.381 0.00 0.00 41.67 2.85
2912 6462 3.625232 CGGTCACCGTGTGTTCTG 58.375 61.111 8.54 1.98 42.73 3.02
2927 6477 6.141211 CGTGTGTTCTGAACTTTTCATCAATG 59.859 38.462 20.18 0.00 39.30 2.82
2933 6483 7.878477 TCTGAACTTTTCATCAATGAATTGC 57.122 32.000 6.27 0.00 45.30 3.56
2972 6527 2.305927 ACAATCCCATCTCCAAAGTCGT 59.694 45.455 0.00 0.00 0.00 4.34
3009 6565 0.096454 GCGTCTGAATTAACGGCACC 59.904 55.000 8.89 0.00 39.24 5.01
3028 6584 2.277501 GCGCCGCAGCATTAACAG 60.278 61.111 3.15 0.00 39.83 3.16
3041 6597 4.216257 AGCATTAACAGAGCGAAAACACAT 59.784 37.500 0.00 0.00 0.00 3.21
3073 6629 2.431771 CACGGACGTGCGGATTCA 60.432 61.111 32.46 0.00 39.39 2.57
3086 6653 2.689983 GCGGATTCACAAATGAGGGAAT 59.310 45.455 0.00 0.00 35.83 3.01
3187 6757 0.400594 GTGGCCAAGTGGGAGTACTT 59.599 55.000 7.24 0.00 41.37 2.24
3231 6801 5.539048 AGTAAGCGACTGTTTACTGAATGT 58.461 37.500 4.12 0.00 46.39 2.71
3232 6802 4.732285 AAGCGACTGTTTACTGAATGTG 57.268 40.909 0.00 0.00 0.00 3.21
3413 7011 0.179076 TATCGTGATGGGCTGCAGTG 60.179 55.000 16.64 0.00 0.00 3.66
3420 7018 4.666253 GGGCTGCAGTGGAGGCAA 62.666 66.667 33.61 0.00 41.39 4.52
3432 7030 4.701651 CAGTGGAGGCAATATTTGTTCTGA 59.298 41.667 0.00 0.00 0.00 3.27
3452 7050 4.985538 TGAGAAGATACATATTTGGGCCC 58.014 43.478 17.59 17.59 0.00 5.80
3464 7062 4.115199 GGGCCCTGGTGTAGCCTG 62.115 72.222 17.04 0.00 46.31 4.85
3508 7106 9.331282 CCTTGAAAGGGAAGAGTATATTTGTAG 57.669 37.037 0.76 0.00 42.66 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.623060 ACTGAACCTGTATTTGCGCATAG 59.377 43.478 12.75 5.04 0.00 2.23
23 24 3.605634 ACTGAACCTGTATTTGCGCATA 58.394 40.909 12.75 7.07 0.00 3.14
24 25 2.436417 ACTGAACCTGTATTTGCGCAT 58.564 42.857 12.75 0.00 0.00 4.73
25 26 1.890876 ACTGAACCTGTATTTGCGCA 58.109 45.000 5.66 5.66 0.00 6.09
26 27 2.989422 AACTGAACCTGTATTTGCGC 57.011 45.000 0.00 0.00 0.00 6.09
27 28 4.466828 CTGAAACTGAACCTGTATTTGCG 58.533 43.478 0.00 0.00 0.00 4.85
28 29 4.229876 GCTGAAACTGAACCTGTATTTGC 58.770 43.478 0.00 0.00 0.00 3.68
29 30 5.215160 GTGCTGAAACTGAACCTGTATTTG 58.785 41.667 0.00 0.00 0.00 2.32
30 31 4.887071 TGTGCTGAAACTGAACCTGTATTT 59.113 37.500 0.00 0.00 0.00 1.40
31 32 4.275936 GTGTGCTGAAACTGAACCTGTATT 59.724 41.667 0.00 0.00 0.00 1.89
32 33 3.815401 GTGTGCTGAAACTGAACCTGTAT 59.185 43.478 0.00 0.00 0.00 2.29
33 34 3.202906 GTGTGCTGAAACTGAACCTGTA 58.797 45.455 0.00 0.00 0.00 2.74
34 35 2.017049 GTGTGCTGAAACTGAACCTGT 58.983 47.619 0.00 0.00 0.00 4.00
35 36 2.016318 TGTGTGCTGAAACTGAACCTG 58.984 47.619 0.00 0.00 0.00 4.00
36 37 2.418368 TGTGTGCTGAAACTGAACCT 57.582 45.000 0.00 0.00 0.00 3.50
37 38 3.715628 AATGTGTGCTGAAACTGAACC 57.284 42.857 0.00 0.00 0.00 3.62
67 68 9.745018 AGGAGACAATTATCATTTCAGAAGAAA 57.255 29.630 0.00 0.00 46.90 2.52
68 69 9.388506 GAGGAGACAATTATCATTTCAGAAGAA 57.611 33.333 0.00 0.00 0.00 2.52
69 70 8.542926 TGAGGAGACAATTATCATTTCAGAAGA 58.457 33.333 0.00 0.00 0.00 2.87
70 71 8.728337 TGAGGAGACAATTATCATTTCAGAAG 57.272 34.615 0.00 0.00 0.00 2.85
71 72 9.690913 AATGAGGAGACAATTATCATTTCAGAA 57.309 29.630 0.00 0.00 37.31 3.02
72 73 9.334947 GAATGAGGAGACAATTATCATTTCAGA 57.665 33.333 0.00 0.00 39.90 3.27
73 74 9.339850 AGAATGAGGAGACAATTATCATTTCAG 57.660 33.333 0.00 0.00 39.90 3.02
74 75 9.690913 AAGAATGAGGAGACAATTATCATTTCA 57.309 29.630 0.00 0.00 39.90 2.69
78 79 9.917887 AGAAAAGAATGAGGAGACAATTATCAT 57.082 29.630 0.00 0.00 32.11 2.45
83 84 9.972106 ATCTTAGAAAAGAATGAGGAGACAATT 57.028 29.630 0.00 0.00 44.75 2.32
84 85 9.393512 CATCTTAGAAAAGAATGAGGAGACAAT 57.606 33.333 0.00 0.00 44.75 2.71
85 86 7.826252 CCATCTTAGAAAAGAATGAGGAGACAA 59.174 37.037 0.00 0.00 44.75 3.18
86 87 7.334090 CCATCTTAGAAAAGAATGAGGAGACA 58.666 38.462 0.00 0.00 44.75 3.41
87 88 6.259829 GCCATCTTAGAAAAGAATGAGGAGAC 59.740 42.308 0.00 0.00 44.75 3.36
88 89 6.157645 AGCCATCTTAGAAAAGAATGAGGAGA 59.842 38.462 0.00 0.00 44.75 3.71
89 90 6.355747 AGCCATCTTAGAAAAGAATGAGGAG 58.644 40.000 0.00 0.00 44.75 3.69
90 91 6.319048 AGCCATCTTAGAAAAGAATGAGGA 57.681 37.500 0.00 0.00 44.75 3.71
91 92 6.600822 TGAAGCCATCTTAGAAAAGAATGAGG 59.399 38.462 0.00 0.00 44.75 3.86
92 93 7.621428 TGAAGCCATCTTAGAAAAGAATGAG 57.379 36.000 0.00 0.00 44.75 2.90
93 94 8.585471 ATTGAAGCCATCTTAGAAAAGAATGA 57.415 30.769 0.00 0.00 44.75 2.57
96 97 9.466497 ACATATTGAAGCCATCTTAGAAAAGAA 57.534 29.630 0.00 0.00 44.75 2.52
97 98 9.466497 AACATATTGAAGCCATCTTAGAAAAGA 57.534 29.630 0.00 0.00 45.63 2.52
100 101 9.241919 TGAAACATATTGAAGCCATCTTAGAAA 57.758 29.630 0.00 0.00 31.48 2.52
101 102 8.806429 TGAAACATATTGAAGCCATCTTAGAA 57.194 30.769 0.00 0.00 31.48 2.10
102 103 8.267183 TCTGAAACATATTGAAGCCATCTTAGA 58.733 33.333 0.00 0.00 31.48 2.10
103 104 8.442632 TCTGAAACATATTGAAGCCATCTTAG 57.557 34.615 0.00 0.00 31.48 2.18
104 105 8.049117 ACTCTGAAACATATTGAAGCCATCTTA 58.951 33.333 0.00 0.00 31.48 2.10
105 106 6.888632 ACTCTGAAACATATTGAAGCCATCTT 59.111 34.615 0.00 0.00 34.68 2.40
106 107 6.421485 ACTCTGAAACATATTGAAGCCATCT 58.579 36.000 0.00 0.00 0.00 2.90
107 108 6.690194 ACTCTGAAACATATTGAAGCCATC 57.310 37.500 0.00 0.00 0.00 3.51
108 109 7.776969 ACATACTCTGAAACATATTGAAGCCAT 59.223 33.333 0.00 0.00 0.00 4.40
109 110 7.112122 ACATACTCTGAAACATATTGAAGCCA 58.888 34.615 0.00 0.00 0.00 4.75
110 111 7.254932 GGACATACTCTGAAACATATTGAAGCC 60.255 40.741 0.00 0.00 0.00 4.35
111 112 7.280876 TGGACATACTCTGAAACATATTGAAGC 59.719 37.037 0.00 0.00 0.00 3.86
112 113 8.722480 TGGACATACTCTGAAACATATTGAAG 57.278 34.615 0.00 0.00 0.00 3.02
113 114 9.685276 AATGGACATACTCTGAAACATATTGAA 57.315 29.630 0.00 0.00 0.00 2.69
114 115 9.112725 CAATGGACATACTCTGAAACATATTGA 57.887 33.333 0.00 0.00 0.00 2.57
115 116 8.896744 ACAATGGACATACTCTGAAACATATTG 58.103 33.333 0.00 0.00 0.00 1.90
116 117 9.466497 AACAATGGACATACTCTGAAACATATT 57.534 29.630 0.00 0.00 0.00 1.28
118 119 9.952030 TTAACAATGGACATACTCTGAAACATA 57.048 29.630 0.00 0.00 0.00 2.29
119 120 8.862325 TTAACAATGGACATACTCTGAAACAT 57.138 30.769 0.00 0.00 0.00 2.71
120 121 7.936847 ACTTAACAATGGACATACTCTGAAACA 59.063 33.333 0.00 0.00 0.00 2.83
121 122 8.324163 ACTTAACAATGGACATACTCTGAAAC 57.676 34.615 0.00 0.00 0.00 2.78
122 123 8.918202 AACTTAACAATGGACATACTCTGAAA 57.082 30.769 0.00 0.00 0.00 2.69
123 124 8.154203 TGAACTTAACAATGGACATACTCTGAA 58.846 33.333 0.00 0.00 0.00 3.02
124 125 7.676004 TGAACTTAACAATGGACATACTCTGA 58.324 34.615 0.00 0.00 0.00 3.27
125 126 7.819415 TCTGAACTTAACAATGGACATACTCTG 59.181 37.037 0.00 0.00 0.00 3.35
126 127 7.907389 TCTGAACTTAACAATGGACATACTCT 58.093 34.615 0.00 0.00 0.00 3.24
127 128 8.607459 CATCTGAACTTAACAATGGACATACTC 58.393 37.037 0.00 0.00 0.00 2.59
128 129 7.554118 CCATCTGAACTTAACAATGGACATACT 59.446 37.037 0.00 0.00 36.58 2.12
129 130 7.336931 ACCATCTGAACTTAACAATGGACATAC 59.663 37.037 6.21 0.00 37.64 2.39
130 131 7.336679 CACCATCTGAACTTAACAATGGACATA 59.663 37.037 6.21 0.00 37.64 2.29
131 132 6.151648 CACCATCTGAACTTAACAATGGACAT 59.848 38.462 6.21 0.00 37.64 3.06
132 133 5.473162 CACCATCTGAACTTAACAATGGACA 59.527 40.000 6.21 0.00 37.64 4.02
133 134 5.619981 GCACCATCTGAACTTAACAATGGAC 60.620 44.000 6.21 0.00 37.64 4.02
134 135 4.458989 GCACCATCTGAACTTAACAATGGA 59.541 41.667 6.21 0.00 37.64 3.41
135 136 4.380867 GGCACCATCTGAACTTAACAATGG 60.381 45.833 0.00 0.00 39.62 3.16
136 137 4.218200 TGGCACCATCTGAACTTAACAATG 59.782 41.667 0.00 0.00 0.00 2.82
137 138 4.406456 TGGCACCATCTGAACTTAACAAT 58.594 39.130 0.00 0.00 0.00 2.71
138 139 3.826524 TGGCACCATCTGAACTTAACAA 58.173 40.909 0.00 0.00 0.00 2.83
139 140 3.500448 TGGCACCATCTGAACTTAACA 57.500 42.857 0.00 0.00 0.00 2.41
140 141 3.057526 GGTTGGCACCATCTGAACTTAAC 60.058 47.826 0.00 0.00 43.61 2.01
141 142 3.153919 GGTTGGCACCATCTGAACTTAA 58.846 45.455 0.00 0.00 43.61 1.85
142 143 2.790433 GGTTGGCACCATCTGAACTTA 58.210 47.619 0.00 0.00 43.61 2.24
143 144 1.620822 GGTTGGCACCATCTGAACTT 58.379 50.000 0.00 0.00 43.61 2.66
144 145 3.346426 GGTTGGCACCATCTGAACT 57.654 52.632 0.00 0.00 43.61 3.01
153 154 1.767759 ATCAAGCATAGGTTGGCACC 58.232 50.000 8.81 0.00 44.67 5.01
154 155 4.981806 TTTATCAAGCATAGGTTGGCAC 57.018 40.909 8.81 0.00 40.81 5.01
155 156 6.543430 AATTTTATCAAGCATAGGTTGGCA 57.457 33.333 8.81 0.00 40.81 4.92
156 157 9.546428 AATAAATTTTATCAAGCATAGGTTGGC 57.454 29.630 8.81 0.00 40.81 4.52
191 192 9.232473 ACTCTCTTTGACAAAGTTAAAAGTCTT 57.768 29.630 23.78 4.11 39.52 3.01
192 193 8.794335 ACTCTCTTTGACAAAGTTAAAAGTCT 57.206 30.769 23.78 4.60 39.52 3.24
193 194 9.917872 GTACTCTCTTTGACAAAGTTAAAAGTC 57.082 33.333 23.78 12.36 39.52 3.01
194 195 9.444600 TGTACTCTCTTTGACAAAGTTAAAAGT 57.555 29.630 23.78 20.33 39.52 2.66
200 201 9.614792 AAACTATGTACTCTCTTTGACAAAGTT 57.385 29.630 23.78 11.75 39.52 2.66
243 244 5.922544 CACCCAAAACTAAATCAAGAGCTTG 59.077 40.000 3.87 3.87 41.71 4.01
244 245 5.011023 CCACCCAAAACTAAATCAAGAGCTT 59.989 40.000 0.00 0.00 0.00 3.74
245 246 4.524328 CCACCCAAAACTAAATCAAGAGCT 59.476 41.667 0.00 0.00 0.00 4.09
246 247 4.522789 TCCACCCAAAACTAAATCAAGAGC 59.477 41.667 0.00 0.00 0.00 4.09
247 248 6.648879 TTCCACCCAAAACTAAATCAAGAG 57.351 37.500 0.00 0.00 0.00 2.85
248 249 7.610580 ATTTCCACCCAAAACTAAATCAAGA 57.389 32.000 0.00 0.00 0.00 3.02
249 250 8.364142 TGTATTTCCACCCAAAACTAAATCAAG 58.636 33.333 0.00 0.00 0.00 3.02
250 251 8.251383 TGTATTTCCACCCAAAACTAAATCAA 57.749 30.769 0.00 0.00 0.00 2.57
251 252 7.841282 TGTATTTCCACCCAAAACTAAATCA 57.159 32.000 0.00 0.00 0.00 2.57
359 360 9.060347 CGTACTACTACCTAGTCAATGGAAATA 57.940 37.037 0.00 0.00 36.95 1.40
360 361 7.559170 ACGTACTACTACCTAGTCAATGGAAAT 59.441 37.037 0.00 0.00 36.95 2.17
361 362 6.886459 ACGTACTACTACCTAGTCAATGGAAA 59.114 38.462 0.00 0.00 36.95 3.13
362 363 6.418101 ACGTACTACTACCTAGTCAATGGAA 58.582 40.000 0.00 0.00 36.95 3.53
363 364 5.994250 ACGTACTACTACCTAGTCAATGGA 58.006 41.667 0.00 0.00 36.95 3.41
364 365 6.690194 AACGTACTACTACCTAGTCAATGG 57.310 41.667 0.00 0.00 36.95 3.16
365 366 7.755591 TGAAACGTACTACTACCTAGTCAATG 58.244 38.462 0.00 0.00 36.95 2.82
366 367 7.928307 TGAAACGTACTACTACCTAGTCAAT 57.072 36.000 0.00 0.00 36.95 2.57
367 368 7.391554 ACATGAAACGTACTACTACCTAGTCAA 59.608 37.037 0.00 0.00 36.95 3.18
368 369 6.881065 ACATGAAACGTACTACTACCTAGTCA 59.119 38.462 0.00 0.00 36.95 3.41
369 370 7.313951 ACATGAAACGTACTACTACCTAGTC 57.686 40.000 0.00 0.00 36.95 2.59
370 371 7.010552 CGTACATGAAACGTACTACTACCTAGT 59.989 40.741 14.44 0.00 37.64 2.57
371 372 7.340699 CGTACATGAAACGTACTACTACCTAG 58.659 42.308 14.44 0.00 37.64 3.02
372 373 7.234187 CGTACATGAAACGTACTACTACCTA 57.766 40.000 14.44 0.00 37.64 3.08
373 374 6.111768 CGTACATGAAACGTACTACTACCT 57.888 41.667 14.44 0.00 37.64 3.08
384 385 4.770351 TGCATCATACGTACATGAAACG 57.230 40.909 19.02 19.02 45.64 3.60
385 386 6.285790 TCATGCATCATACGTACATGAAAC 57.714 37.500 18.28 9.14 42.93 2.78
388 389 6.222389 TCATTCATGCATCATACGTACATGA 58.778 36.000 17.22 17.22 43.87 3.07
389 390 6.470557 TCATTCATGCATCATACGTACATG 57.529 37.500 13.97 13.97 39.53 3.21
390 391 7.677454 AATCATTCATGCATCATACGTACAT 57.323 32.000 0.00 0.00 0.00 2.29
391 392 8.658609 CATAATCATTCATGCATCATACGTACA 58.341 33.333 0.00 0.00 0.00 2.90
392 393 8.872845 TCATAATCATTCATGCATCATACGTAC 58.127 33.333 0.00 0.00 0.00 3.67
393 394 8.872845 GTCATAATCATTCATGCATCATACGTA 58.127 33.333 0.00 0.00 0.00 3.57
394 395 7.148356 GGTCATAATCATTCATGCATCATACGT 60.148 37.037 0.00 0.00 0.00 3.57
395 396 7.184779 GGTCATAATCATTCATGCATCATACG 58.815 38.462 0.00 0.00 0.00 3.06
396 397 7.478322 GGGTCATAATCATTCATGCATCATAC 58.522 38.462 0.00 0.00 0.00 2.39
397 398 6.316890 CGGGTCATAATCATTCATGCATCATA 59.683 38.462 0.00 0.00 0.00 2.15
398 399 5.124936 CGGGTCATAATCATTCATGCATCAT 59.875 40.000 0.00 0.00 0.00 2.45
399 400 4.456566 CGGGTCATAATCATTCATGCATCA 59.543 41.667 0.00 0.00 0.00 3.07
400 401 4.673580 GCGGGTCATAATCATTCATGCATC 60.674 45.833 0.00 0.00 0.00 3.91
401 402 3.192001 GCGGGTCATAATCATTCATGCAT 59.808 43.478 0.00 0.00 0.00 3.96
402 403 2.553602 GCGGGTCATAATCATTCATGCA 59.446 45.455 0.00 0.00 0.00 3.96
403 404 2.553602 TGCGGGTCATAATCATTCATGC 59.446 45.455 0.00 0.00 0.00 4.06
404 405 4.456566 TCATGCGGGTCATAATCATTCATG 59.543 41.667 0.00 0.00 33.19 3.07
405 406 4.654915 TCATGCGGGTCATAATCATTCAT 58.345 39.130 0.00 0.00 33.19 2.57
406 407 4.084011 TCATGCGGGTCATAATCATTCA 57.916 40.909 0.00 0.00 33.19 2.57
407 408 6.932356 ATATCATGCGGGTCATAATCATTC 57.068 37.500 0.00 0.00 33.19 2.67
408 409 7.707624 AAATATCATGCGGGTCATAATCATT 57.292 32.000 0.00 0.00 33.19 2.57
409 410 8.049117 AGTAAATATCATGCGGGTCATAATCAT 58.951 33.333 0.00 0.00 33.19 2.45
410 411 7.394016 AGTAAATATCATGCGGGTCATAATCA 58.606 34.615 0.00 0.00 33.19 2.57
411 412 7.849804 AGTAAATATCATGCGGGTCATAATC 57.150 36.000 0.00 0.00 33.19 1.75
412 413 8.540388 AGTAGTAAATATCATGCGGGTCATAAT 58.460 33.333 0.00 0.00 33.19 1.28
413 414 7.903145 AGTAGTAAATATCATGCGGGTCATAA 58.097 34.615 0.00 0.00 33.19 1.90
414 415 7.363530 GGAGTAGTAAATATCATGCGGGTCATA 60.364 40.741 0.00 0.00 33.19 2.15
415 416 6.360370 AGTAGTAAATATCATGCGGGTCAT 57.640 37.500 0.00 0.00 35.31 3.06
416 417 5.279306 GGAGTAGTAAATATCATGCGGGTCA 60.279 44.000 0.00 0.00 0.00 4.02
417 418 5.047235 AGGAGTAGTAAATATCATGCGGGTC 60.047 44.000 0.00 0.00 0.00 4.46
418 419 4.838986 AGGAGTAGTAAATATCATGCGGGT 59.161 41.667 0.00 0.00 0.00 5.28
419 420 5.407407 AGGAGTAGTAAATATCATGCGGG 57.593 43.478 0.00 0.00 0.00 6.13
420 421 6.477033 GCATAGGAGTAGTAAATATCATGCGG 59.523 42.308 0.00 0.00 0.00 5.69
421 422 7.035612 TGCATAGGAGTAGTAAATATCATGCG 58.964 38.462 0.00 0.00 38.25 4.73
422 423 8.037758 ACTGCATAGGAGTAGTAAATATCATGC 58.962 37.037 0.00 0.00 32.49 4.06
423 424 9.935241 AACTGCATAGGAGTAGTAAATATCATG 57.065 33.333 0.00 0.00 33.14 3.07
424 425 9.935241 CAACTGCATAGGAGTAGTAAATATCAT 57.065 33.333 0.00 0.00 33.14 2.45
425 426 9.143155 TCAACTGCATAGGAGTAGTAAATATCA 57.857 33.333 0.00 0.00 33.14 2.15
433 434 9.314133 TCATATTATCAACTGCATAGGAGTAGT 57.686 33.333 0.00 0.00 35.93 2.73
436 437 9.851686 TTTTCATATTATCAACTGCATAGGAGT 57.148 29.630 0.00 0.00 0.00 3.85
443 444 9.340695 CGTTTCTTTTTCATATTATCAACTGCA 57.659 29.630 0.00 0.00 0.00 4.41
444 445 9.554724 TCGTTTCTTTTTCATATTATCAACTGC 57.445 29.630 0.00 0.00 0.00 4.40
455 456 9.372369 ACCACAAAAATTCGTTTCTTTTTCATA 57.628 25.926 0.00 0.00 33.49 2.15
456 457 8.262715 ACCACAAAAATTCGTTTCTTTTTCAT 57.737 26.923 0.00 0.00 33.49 2.57
457 458 7.659652 ACCACAAAAATTCGTTTCTTTTTCA 57.340 28.000 0.00 0.00 33.49 2.69
458 459 9.467990 GTTACCACAAAAATTCGTTTCTTTTTC 57.532 29.630 0.00 0.00 33.49 2.29
459 460 8.163516 CGTTACCACAAAAATTCGTTTCTTTTT 58.836 29.630 0.00 0.00 35.51 1.94
460 461 7.541437 TCGTTACCACAAAAATTCGTTTCTTTT 59.459 29.630 0.00 0.00 0.00 2.27
461 462 7.028361 TCGTTACCACAAAAATTCGTTTCTTT 58.972 30.769 0.00 0.00 0.00 2.52
462 463 6.553524 TCGTTACCACAAAAATTCGTTTCTT 58.446 32.000 0.00 0.00 0.00 2.52
463 464 6.121613 TCGTTACCACAAAAATTCGTTTCT 57.878 33.333 0.00 0.00 0.00 2.52
464 465 6.793479 TTCGTTACCACAAAAATTCGTTTC 57.207 33.333 0.00 0.00 0.00 2.78
465 466 7.411696 GGTTTTCGTTACCACAAAAATTCGTTT 60.412 33.333 0.00 0.00 35.67 3.60
466 467 6.034790 GGTTTTCGTTACCACAAAAATTCGTT 59.965 34.615 0.00 0.00 35.67 3.85
467 468 5.515982 GGTTTTCGTTACCACAAAAATTCGT 59.484 36.000 0.00 0.00 35.67 3.85
468 469 5.515626 TGGTTTTCGTTACCACAAAAATTCG 59.484 36.000 0.00 0.00 40.65 3.34
469 470 6.889019 TGGTTTTCGTTACCACAAAAATTC 57.111 33.333 0.00 0.00 40.65 2.17
479 480 2.490115 TGCATGGATGGTTTTCGTTACC 59.510 45.455 0.00 0.00 36.17 2.85
480 481 3.840890 TGCATGGATGGTTTTCGTTAC 57.159 42.857 0.00 0.00 0.00 2.50
481 482 3.428725 GCATGCATGGATGGTTTTCGTTA 60.429 43.478 27.34 0.00 0.00 3.18
482 483 2.674747 GCATGCATGGATGGTTTTCGTT 60.675 45.455 27.34 0.00 0.00 3.85
483 484 1.135024 GCATGCATGGATGGTTTTCGT 60.135 47.619 27.34 0.00 0.00 3.85
484 485 1.135053 TGCATGCATGGATGGTTTTCG 60.135 47.619 27.34 1.90 0.00 3.46
485 486 2.546778 CTGCATGCATGGATGGTTTTC 58.453 47.619 27.34 11.31 0.00 2.29
486 487 1.406341 GCTGCATGCATGGATGGTTTT 60.406 47.619 27.34 0.00 42.31 2.43
487 488 0.177141 GCTGCATGCATGGATGGTTT 59.823 50.000 27.34 0.00 42.31 3.27
488 489 1.682451 GGCTGCATGCATGGATGGTT 61.682 55.000 27.34 0.00 45.15 3.67
489 490 2.131709 GGCTGCATGCATGGATGGT 61.132 57.895 27.34 0.00 45.15 3.55
490 491 2.734591 GGCTGCATGCATGGATGG 59.265 61.111 27.34 15.17 45.15 3.51
491 492 2.734591 GGGCTGCATGCATGGATG 59.265 61.111 27.34 21.79 45.15 3.51
492 493 2.523412 GGGGCTGCATGCATGGAT 60.523 61.111 27.34 0.00 45.15 3.41
493 494 4.845447 GGGGGCTGCATGCATGGA 62.845 66.667 27.34 23.99 45.15 3.41
562 563 0.107654 ACCATCCGGCTGCTTAAGTC 60.108 55.000 4.02 0.00 34.57 3.01
563 564 0.392998 CACCATCCGGCTGCTTAAGT 60.393 55.000 4.02 0.00 34.57 2.24
589 591 2.741985 TCATGGTGCCGTTCGCTG 60.742 61.111 0.00 0.00 38.78 5.18
591 593 4.147322 CGTCATGGTGCCGTTCGC 62.147 66.667 0.00 0.00 38.31 4.70
615 617 1.386533 GATGAACAGCACCATCCAGG 58.613 55.000 0.00 0.00 45.67 4.45
623 625 0.391130 TACTGCCGGATGAACAGCAC 60.391 55.000 5.05 0.00 34.72 4.40
626 628 1.871080 GGATACTGCCGGATGAACAG 58.129 55.000 5.05 4.80 37.45 3.16
636 638 2.728817 CTCGGTCCGGATACTGCC 59.271 66.667 7.81 1.90 0.00 4.85
653 655 3.316308 AGTCTGATGGTCAACTTGTTTGC 59.684 43.478 0.00 0.00 34.88 3.68
656 658 4.422073 TGAGTCTGATGGTCAACTTGTT 57.578 40.909 0.00 0.00 0.00 2.83
865 874 5.678955 AGAAACGGAGGAGCTAGTAATTT 57.321 39.130 0.00 0.00 0.00 1.82
897 912 0.824759 CTAGGTAGCTTTCCTGGCGT 59.175 55.000 17.04 0.00 36.60 5.68
926 945 0.962855 GAGGGAAGGCTTGGCTCAAC 60.963 60.000 3.46 0.00 0.00 3.18
929 948 1.077858 CAGAGGGAAGGCTTGGCTC 60.078 63.158 3.46 0.00 0.00 4.70
937 956 2.285668 TGGGAGGCAGAGGGAAGG 60.286 66.667 0.00 0.00 0.00 3.46
938 957 2.674220 GGTGGGAGGCAGAGGGAAG 61.674 68.421 0.00 0.00 0.00 3.46
939 958 2.610859 GGTGGGAGGCAGAGGGAA 60.611 66.667 0.00 0.00 0.00 3.97
940 959 3.194025 AAGGTGGGAGGCAGAGGGA 62.194 63.158 0.00 0.00 0.00 4.20
941 960 2.612115 AAGGTGGGAGGCAGAGGG 60.612 66.667 0.00 0.00 0.00 4.30
942 961 1.204113 AAGAAGGTGGGAGGCAGAGG 61.204 60.000 0.00 0.00 0.00 3.69
943 962 0.695347 AAAGAAGGTGGGAGGCAGAG 59.305 55.000 0.00 0.00 0.00 3.35
944 963 0.401738 CAAAGAAGGTGGGAGGCAGA 59.598 55.000 0.00 0.00 0.00 4.26
945 964 1.246737 GCAAAGAAGGTGGGAGGCAG 61.247 60.000 0.00 0.00 0.00 4.85
946 965 1.228552 GCAAAGAAGGTGGGAGGCA 60.229 57.895 0.00 0.00 0.00 4.75
947 966 0.962855 GAGCAAAGAAGGTGGGAGGC 60.963 60.000 0.00 0.00 0.00 4.70
984 1016 2.243994 GCCCATTCCCTTTAGGTAGGTT 59.756 50.000 0.00 0.00 36.75 3.50
996 1028 2.761213 CCCAAGCTGCCCATTCCC 60.761 66.667 0.00 0.00 0.00 3.97
1065 1097 2.291043 ATCTTCGGGGTTGAGCGGT 61.291 57.895 0.00 0.00 0.00 5.68
1437 1469 0.472925 TGGGTAGGTGCAGGAGTTGA 60.473 55.000 0.00 0.00 0.00 3.18
1448 1480 0.991920 CATGAAGGTGGTGGGTAGGT 59.008 55.000 0.00 0.00 0.00 3.08
1689 1721 2.443390 CCGGTAGGGATGGACCGT 60.443 66.667 12.05 0.00 43.50 4.83
2251 2283 1.048601 AACCTATCATCGGCGTGGAT 58.951 50.000 17.11 17.11 0.00 3.41
2256 2288 1.202533 ACCTCAAACCTATCATCGGCG 60.203 52.381 0.00 0.00 0.00 6.46
2338 2370 2.427245 CCTCGTCGGCATCCTCCTT 61.427 63.158 0.00 0.00 0.00 3.36
2668 2727 5.809001 ACCTTCGGTCGGTATATGTAGATA 58.191 41.667 0.00 0.00 31.69 1.98
2678 2740 8.840321 GCTATATATATAAACCTTCGGTCGGTA 58.160 37.037 4.06 0.00 33.12 4.02
2679 2741 7.340232 TGCTATATATATAAACCTTCGGTCGGT 59.660 37.037 4.06 0.00 33.12 4.69
2688 2750 5.903589 ACCGGCCTGCTATATATATAAACCT 59.096 40.000 0.00 0.00 0.00 3.50
2692 2754 6.375418 TGGTACCGGCCTGCTATATATATAA 58.625 40.000 7.57 0.00 0.00 0.98
2789 6335 1.468224 CGTCACTCGCAAGCAGAGTAT 60.468 52.381 15.36 0.00 46.16 2.12
2799 6345 1.969809 GCATGCATTCGTCACTCGCA 61.970 55.000 14.21 0.00 39.67 5.10
2819 6365 1.257415 CTTCTTGATCGAGATGCGTGC 59.743 52.381 13.61 0.00 41.80 5.34
2839 6389 4.367386 ACCTACTGAGTGCAACGTATAC 57.633 45.455 0.00 0.00 45.86 1.47
2927 6477 3.681897 CGGCATGTAGATAGGAGCAATTC 59.318 47.826 0.00 0.00 0.00 2.17
2933 6483 4.848562 TTGTACGGCATGTAGATAGGAG 57.151 45.455 0.00 0.00 32.51 3.69
2990 6546 0.096454 GGTGCCGTTAATTCAGACGC 59.904 55.000 4.06 1.90 37.91 5.19
3028 6584 2.143122 TCTGACCATGTGTTTTCGCTC 58.857 47.619 0.00 0.00 0.00 5.03
3041 6597 1.483004 TCCGTGTCAAAACTCTGACCA 59.517 47.619 1.54 0.00 44.30 4.02
3073 6629 3.118775 TGTCGATCGATTCCCTCATTTGT 60.119 43.478 22.50 0.00 0.00 2.83
3086 6653 6.961359 AACATGAAATTACTTGTCGATCGA 57.039 33.333 15.15 15.15 0.00 3.59
3144 6714 6.476706 ACTTGTATTTCTGCTTTGCTTTGTTC 59.523 34.615 0.00 0.00 0.00 3.18
3187 6757 9.610705 CTTACTACTGTAGTATTGTCCTACTCA 57.389 37.037 24.04 7.67 40.66 3.41
3231 6801 2.550606 GTTGCAAGTACCAATCGTTCCA 59.449 45.455 0.00 0.00 0.00 3.53
3232 6802 2.095415 GGTTGCAAGTACCAATCGTTCC 60.095 50.000 0.00 0.00 35.67 3.62
3413 7011 5.882557 TCTTCTCAGAACAAATATTGCCTCC 59.117 40.000 0.00 0.00 0.00 4.30
3432 7030 4.202609 CCAGGGCCCAAATATGTATCTTCT 60.203 45.833 27.56 0.00 0.00 2.85
3452 7050 0.108585 ACCAACACAGGCTACACCAG 59.891 55.000 0.00 0.00 43.14 4.00
3464 7062 1.733526 GGGCTCACACAACCAACAC 59.266 57.895 0.00 0.00 0.00 3.32
3492 7090 7.011482 CACCCAAGTGCTACAAATATACTCTTC 59.989 40.741 0.00 0.00 37.14 2.87
3494 7092 6.349300 CACCCAAGTGCTACAAATATACTCT 58.651 40.000 0.00 0.00 37.14 3.24
3495 7093 6.604735 CACCCAAGTGCTACAAATATACTC 57.395 41.667 0.00 0.00 37.14 2.59


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.